R version 4.5.0 RC (2025-04-04 r88112 ucrt) -- "How About a Twenty-Six"
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> library("aroma.apd")
Loading required package: affxparser
aroma.apd v0.7.1 successfully loaded. See ?aroma.apd for help.
> library("R.utils") # Arguments
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.27.0 (2024-11-01 18:00:02 UTC) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following object is masked from 'package:R.methodsS3':

    throw

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, load, save

R.utils v2.13.0 (2025-02-24 21:20:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:affxparser':

    findFiles

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, isOpen, nullfile, parse, use, warnings

> 
> verbose <- Arguments$getVerbose(TRUE)
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # 1. Scan for existing CEL files
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # a) Scan current directory for CEL files
> files <- list.files(pattern="[.](cel|CEL)$")
> files <- files[!file.info(files)$isdir]
> if (length(files) > 0 && require("affxparser")) {
+   # b) Corresponding APD filenames
+   celNames <- files
+   apdNames <- gsub(pattern, ".apd", files)
+ 
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 1. Copy the probe intensities from a CEL to an APD file
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   for (kk in 1) {
+     verbose && enter(verbose, "Reading CEL file #", kk)
+     cel <- readCel(celNames[kk])
+     verbose && exit(verbose)
+ 
+     chipType <- cel$header$chiptype
+     verbose && enter(verbose, "Getting read map for '", chipType, "'")
+     mapType <- chipType
+     mapFile <- paste(mapType, ".apm", sep="")
+     if (file.exists(mapFile)) {
+       verbose && enter(verbose, "Reading read map from APD map file")
+       readMap <- readApdMap(mapFile)$map
+       verbose && exit(verbose)
+     } else {
+       verbose && enter(verbose, "Generating read map from CDF file")
+       cdfFile <- findCdf(chipType)
+       readMap <- readCdfUnitsMap(cdfFile)
+       writeApdMap(mapFile, map=readMap)
+       verbose && exit(verbose)
+     }
+     verbose && exit(verbose)
+ 
+     if (!file.exists(apdNames[kk])) {
+       verbose && enter(verbose, "Calculating write map from read map")
+       writeMap <- invertMap(readMap)
+       verbose && exit(verbose)
+ 
+       verbose && enter(verbose, "Creating APD file #", kk)
+       writeApd(apdNames[kk], data=cel$intensities, chipType=chipType,
+                                      mapType=mapType, writeMap=writeMap)
+       verbose && exit(verbose)
+       rm(writeMap)
+     }
+ 
+     verbose && enter(verbose, "Verifying APD file #", kk)
+     apd <- readApd(apdNames[kk], readMap=readMap)
+     verbose && exit(verbose)
+     stopifnot(identical(apd$intensities, cel$intensities))
+ 
+     rm(cel, mapType, mapFile, apd)
+   }
+ 
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 2. Read a subset of the units
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   units <- c(1, 20:205)
+   cel <- readCelUnits(celNames[1], units=units)
+   apd <- readApdUnits(apdNames[1], units=units)
+   stopifnot(identical(apd, cel))
+ 
+ 
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # 3. Benchmark reading with and without read map
+   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+   # To minimize the overhead from searching for and reading CDF
+   # file when benchmarking, we read the CDF already here
+   cdfFile <- findCdf(chipType)
+   cdf <- readCdfCellIndices(cdfFile, units=units)
+ 
+   cat("Benchmarks for read APD file:\n")
+   t0 <- system.time({
+     # Approximately 10 times faster than without a read map
+     apd <- readApdUnits(apdNames[1], cdf=cdf, readMap=readMap)
+   })[3]
+   cat(sprintf("a) with read map by vector: %.3fs [ 1.00x]\n", t0))
+ 
+   t <- system.time({
+     apd <- readApdUnits(apdNames[1], cdf=cdf)
+   })[3]
+   cat(sprintf("b) with read map from file: %.3fs [%5.2fx]\n", t, t/t0))
+ 
+   t <- system.time({
+     # Force no read map to be used
+     apd <- readApdUnits(apdNames[1], cdf=cdf, readMap=NULL)
+   })[3]
+   cat(sprintf("c) without read map       : %.3fs [%5.2fx]\n", t, t/t0))
+ } # if (length(files) > 0)
> 
> proc.time()
   user  system elapsed 
   0.18    0.10    0.28